Does anybody else hate it when in fiction the leader can beat all the teamates
 

Its sort of annoying

Well, their labeled The Leader for a reason, becuase their stronger, faster and usually smarter then the other teammates.
So, no.

Of course Skeletor could beat all of his henchmen/-women. But could Shredder beat all of the foot clan, hundreds, maybe thousands of them?

I think it's really cheap and lame, especially since many of these leaders can't seem to use that same level of skill though out most of the series. I guess that's the word effect.